Timeline



Jul 27, 2026: Today

5:06 PM Ticket #20800 ('rock' frame rate) created by iamkaant@…
From #20432: the framerate of ‘rock’ command isn’t stable, and changes …
3:49 PM Dev2026-07-27 edited by Tom Goddard
(diff)
3:48 PM Dev2026-07-27 edited by Tom Goddard
(diff)
3:03 PM Dev2026-07-27 created by Tom Goddard
3:02 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:49 PM Ticket #20799 (adding "+python-version" breaks toolshed) created by Eric Pettersen
The various config and cache directories changed to add "+python3.14" …
1:21 PM Ticket #20798 (mmCIF reader using defunct ligand-expo.rcsb.org web site) created by goddard@…
[…] fold_2026_07_15_12_10_model_0_LIG_A.cif​
12:18 PM Ticket #20797 (Crash destroying ISOLDE OpenMM thread on exit) created by chimerax-bug-report@…
[…]
12:12 PM Ticket #20793 (Various Match→Align errors) closed by Eric Pettersen
fixed: The first one I cannot reproduce on our Windows box. The second is …
12:06 PM Ticket #20796 (Unknown problem) created by kmanne@…
[…]
11:33 AM Ticket #20791 (Crash trying to tab one dock widget with another) closed by Tom Goddard
nonchimerax: This is the only crash reported containing …

Jul 26, 2026: Yesterday

4:25 PM Ticket #20795 (Crash in manage() call for ArtiaX options window) created by frankma@…
[…]

Jul 25, 2026:

12:08 PM Ticket #20794 (Clipper session restore: self.structure is None) created by srr131@…
[…]
10:24 AM Ticket #20793 (Various Match→Align errors) created by chimerax-bug-report@…
[…]

Jul 24, 2026:

9:25 PM Ticket #20792 (SEQCROW: error reading XYZ file) created by 1806191@…
[…] azIMFPZTMOP_crest_best.xyz​
10:24 AM Ticket #20790 (Douse: name 'compare_model' is not defined) closed by Eric Pettersen
fixed: Hi Max, Thanks for reporting this problem. The problem was in …
10:20 AM Ticket #20791 (Crash trying to tab one dock widget with another) created by chimerax-bug-report@…
[…]
5:11 AM Ticket #20790 (Douse: name 'compare_model' is not defined) created by borgosch@…
[…]

Jul 23, 2026:

5:53 PM Ticket #20762 (Minimization failure: KeyError: 'N') closed by Eric Pettersen
fixed: Hi, Thanks for reporting this problem, the fix will be in tomorrow's …
1:48 PM Ticket #19894 ("align axis" command) closed by Eric Pettersen
fixed: Implemented as "axis align" command in current daily build.
12:17 PM Ticket #20788 (Crash handling event) closed by Tom Goddard
limitation: Looks like the user may have run ChimeraX directly from the DMG and …
11:52 AM Ticket #20783 (ViewDock opening a swissdock file: not enough values to unpack ...) closed by Eric Pettersen
can't reproduce
11:50 AM Ticket #20781 (H-Bonds: acc_phi_psi() bad number of arguments) closed by Eric Pettersen
not a bug: Hi, Your SIRT1_clean.pdb file produced a structure with incorrect …
11:43 AM Ticket #20779 (KVFinder on old MacOS) closed by Eric Pettersen
limitation: Hi Stuti, Unfortunately, the underlying pyKVFinder program that …
11:08 AM Ticket #20789 (Suppress "GBM is not supported..." startup Qt message on Linux) closed by Tom Goddard
fixed: Fixed. We already had a list of about 8 Qt messages that we suppress …
10:57 AM Ticket #20789 (Suppress "GBM is not supported..." startup Qt message on Linux) created by goddard@…
[…]
3:15 AM Ticket #20788 (Crash handling event) created by chimerax-bug-report@…
[…]

Jul 22, 2026:

6:28 PM ChangeLog edited by Tom Goddard
(diff)
6:23 PM ChangeLog edited by Tom Goddard
(diff)
6:21 PM ChangeLog edited by Tom Goddard
(diff)
6:18 PM Ticket #20787 (Add alphafold fetch for mutation scores sequences) closed by Tom Goddard
fixed: Done. If the mutation set is fetched from MaveDB it usually has a …
5:48 PM Ticket #20787 (Add alphafold fetch for mutation scores sequences) created by Tom Goddard
Add a button to the Mutation Scores panel to fetch an AlphaFold …
5:05 PM Ticket #20786 (Added fetching of MaveDB mutation data) closed by Tom Goddard
fixed: Done. MaveDB entry identifiers are 00000001, 00000002, .... I allow …
4:48 PM Ticket #20786 (Added fetching of MaveDB mutation data) created by Tom Goddard
Allow fetching mutation score data from the Multiplexed Assays of …
4:43 PM Ticket #20785 (Allow coloring structure at residues with uniprot variant mutations ...) closed by Tom Goddard
fixed: Done. I added a mutationscores merge command and also added an …
4:02 PM Ticket #20785 (Allow coloring structure at residues with uniprot variant mutations ...) created by Tom Goddard
I'd like to be able to look at deep mutational scan scores for just …
3:51 PM Ticket #20142 (Make a mutation score heatmap GUI) closed by Tom Goddard
fixed: Done. The heatmaps are reasonably usable now. If more improvements …
3:49 PM Ticket #19403 (Add structure coloring controls to mutation scores scatter plot) closed by Tom Goddard
fixed: Done. The mutation score ranges option was documented by Elaine. All …
3:43 PM Ticket #20597 (Opening mutation score .csv file does not show the scores in the order ...) closed by Tom Goddard
fixed: Fixed. I made the scores appear in alphabetical order.
3:40 PM Ticket #20784 (OpenFold prediction fails if model parameters did not download during ...) created by Tom Goddard
In ticket #20783 the anonymous user tries to run several OpenFold …
1:58 PM ChangeLog edited by Eric Pettersen
(diff)
1:58 PM ChangeLog edited by Eric Pettersen
(diff)
1:58 PM ChangeLog edited by Eric Pettersen
(diff)
1:57 PM ChangeLog edited by Eric Pettersen
(diff)
12:22 PM Ticket #20783 (ViewDock opening a swissdock file: not enough values to unpack ...) created by chimerax-bug-report@…
[…]
11:10 AM Ticket #20782 (Python shell debugger warning) closed by Tom Goddard
not a bug
11:03 AM Ticket #20780 (H-Bonds: acc_phi_psi() bad number of arguments) closed by Tom Goddard
duplicate: Same as #20781
11:01 AM Ticket #20777 (KVFinder on old MacOS) closed by Tom Goddard
duplicate: Same as #20779
8:18 AM Ticket #20782 (Python shell debugger warning) created by alexandra.zahradnikova@…
[…]
3:14 AM Ticket #20781 (H-Bonds: acc_phi_psi() bad number of arguments) created by shreyasukar@…
[…]
3:13 AM Ticket #20780 (H-Bonds: acc_phi_psi() bad number of arguments) created by chimerax-bug-report@…
[…]

Jul 21, 2026:

7:47 AM Ticket #20779 (KVFinder on old MacOS) created by stuti_sharma@…
[…]
12:47 AM Ticket #20778 (pyKVFinder: KeyError: 'KAA') created by aleksandr.kharchenko@…
[…]

Jul 20, 2026:

6:16 PM Ticket #20768 (Session save failure) closed by Eric Pettersen
can't reproduce: Hi Lydia, Thanks for reporting this problem and providing the session …
4:12 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:10 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:10 PM Dev2026-07-20 edited by Tom Goddard
(diff)
3:59 PM Ticket #20335 (Python 3.14 changes refcount semantics) closed by Tom Goddard
fixed: Fixed. Only the geometry place.py use of getrefcount() needed fixing. …
3:02 PM Dev2026-07-20 created by Tom Goddard
3:01 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:10 PM Ticket #20773 (Crash in NSAccessibility routines in Qt 6.10.2 and ChimeraX 1.12) closed by Tom Goddard
can't reproduce: I think this the first crash report in Mac accessibility routines in …
11:58 AM Ticket #20777 (KVFinder on old MacOS) created by chimerax-bug-report@…
[…]
10:36 AM Ticket #20776 (Fetch identifier) closed by Eric Pettersen
not a bug: Hi Thu, P0CE95 is not a PDB identifier. As the error message says, …
10:28 AM Ticket #20775 (KVFinder on old MacOS) closed by Eric Pettersen
duplicate
10:20 AM Ticket #20772 (H-Bonds: More than 2 coplanar positions specified) closed by Eric Pettersen
can't reproduce
10:19 AM Ticket #20771 (Minimize: KeyError: 'OP3') closed by Eric Pettersen
can't reproduce
9:08 AM Ticket #20776 (Fetch identifier) created by nguy2883@…
[…]
8:59 AM Ticket #20775 (KVFinder on old MacOS) created by chimerax-bug-report@…
[…]

Jul 19, 2026:

6:25 PM Ticket #20774 (ISOLDLE: validation tab refers to deleted residue) created by john.heumann@…
[…]
8:27 AM Ticket #20773 (Crash in NSAccessibility routines in Qt 6.10.2 and ChimeraX 1.12) created by chimerax-bug-report@…
[…]

Jul 17, 2026:

11:14 PM Ticket #20772 (H-Bonds: More than 2 coplanar positions specified) created by chimerax-bug-report@…
[…]
8:05 PM Ticket #20771 (Minimize: KeyError: 'OP3') created by chimerax-bug-report@…
[…]
12:06 PM Ticket #20770 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: This ChimeraX crash is due to a bug in the Qt window toolkit and …
11:41 AM Ticket #20769 (ArtiaX: read RELION STAR file: Cannot interpret as a data type) closed by Eric Pettersen
duplicate: User was using old version of ArtiaX (0.1).
6:40 AM Ticket #20770 (Crash on Mac waking from sleep) created by goncalvesgm@…
[…]
5:07 AM Ticket #20769 (ArtiaX: read RELION STAR file: Cannot interpret as a data type) created by chimerax-bug-report@…
[…]
3:46 AM Ticket #20768 (Session save failure) created by lydia.godfrey@…
[…] KIF1C mutations chimera.cxs​

Jul 16, 2026:

3:00 PM Ticket #20765 ('measure mapvalues' should disallow illegal/problematic attribute names) closed by Tom Goddard
fixed: Fixed. An error is issued explaining the allowed attribute name …
11:26 AM Ticket #20766 (blast protein: 'return' in a 'finally' block) closed by Zach Pearson
fixed: It may be easy to just patch grako (some more). I moved the return in …
10:05 AM Ticket #20767 (sel <named selection> selects all atoms in chain B) created by mohammad.alhossary@…
[…] log.txt​ wFAP0.pdb​
9:36 AM Ticket #20764 (Multiple consecutive identical commands) closed by Eric Pettersen
can't reproduce: Is this AI driven?
9:35 AM Ticket #20766 (blast protein: 'return' in a 'finally' block) created by Eric Pettersen
[…]
8:59 AM Ticket #20765 ('measure mapvalues' should disallow illegal/problematic attribute names) created by rwaldo@…
[…]
7:53 AM Ticket #20764 (Multiple consecutive identical commands) created by chimerax-bug-report@…
[…]

Jul 15, 2026:

6:06 PM Ticket #20763 (Invalid escape sequence \* warning at startup in volume code) closed by Tom Goddard
fixed
6:05 PM Ticket #20763 (Invalid escape sequence \* warning at startup in volume code) reopened by Tom Goddard
Fixed. Volume save_map() function doc string had \*.cmap and \*.mrc …
5:48 PM Ticket #20763 (Invalid escape sequence \* warning at startup in volume code) closed by Tom Goddard
fixed: I didn't get this warning the second time I started this daily build, …
5:46 PM Ticket #20763 (Invalid escape sequence \* warning at startup in volume code) created by goddard@…
[…]
3:01 PM Ticket #20758 ('zone' command uses dead residue) closed by Tom Goddard
fixed: Fixed. The zone mouse mode gave an error when dragging to increase …
4:29 AM Ticket #20762 (Minimization failure: KeyError: 'N') created by gwshim0189@…
[…]

Jul 14, 2026:

3:44 PM Ticket #20761 (Color blobs mouse mode is choosing transparent colors) closed by Tom Goddard
fixed: Fixed. There was an overflow in the computation of the clicked …
3:15 PM ChangeLog edited by Greg Couch
(diff)
3:06 PM Ticket #20761 (Color blobs mouse mode is choosing transparent colors) created by goddard@…
[…]
2:57 PM Ticket #20760 (TypeError: setChecked(self, a0: bool): argument 1 has unexpected type ...) closed by Tom Goddard
fixed: Fixed. Cast from numpy.bool to Python bool in volume viewer gui code.
2:50 PM Ticket #20760 (TypeError: setChecked(self, a0: bool): argument 1 has unexpected type ...) created by goddard@…
[…]
2:18 PM Ticket #20759 (OpenGL "invalid framebuffer operation" in glclear after display reconnected) created by goddard@…
[…]
2:02 PM Ticket #20600 (Minimization of RNA fails) closed by Eric Pettersen
fixed: Fixed in tomorrow's daily build. Fix: …
12:21 PM Ticket #20758 ('zone' command uses dead residue) created by chimerax-bug-report@…
[…]
10:56 AM Ticket #20750 (numpy bool no longer accepted by QCheckBox.setChecked()) closed by Eric Pettersen
fixed: Fix: …
6:59 AM Ticket #20757 (DLL load failed while importing: An Application Control policy has ...) created by chimerax-bug-report@…
[…]

Jul 13, 2026:

7:07 PM Ticket #20756 (DLL load failed while importing: An Application Control policy has ...) created by chimerax-bug-report@…
[…]
5:49 PM Ticket #20751 (Failed to create D3D11 swapchain) closed by Tom Goddard
nonchimerax: Nvidia graphics driver problem, Windows. I'd try rebooting the …
5:42 PM Ticket #20749 (Save image/movie, no opengl context) closed by Tom Goddard
nonchimerax: There are several problems here. First the user tries "movie encode …
5:27 PM Ticket #20748 (COD bond-perception bug) closed by Greg Couch
duplicate: Duplicate of . Likely fixed by recent change.
5:22 PM Ticket #20605 (glClear: invalid framebuffer operation drawing scene) closed by Tom Goddard
duplicate: This ChimeraX error is caused by a bug in the Mac Qt window toolkit …
5:18 PM Ticket #20755 (The GPU device instance has been suspended) closed by Eric Pettersen
duplicate
5:15 PM Ticket #20754 (The GPU device instance has been suspended) closed by Eric Pettersen
duplicate
4:54 PM Dev2026-07-13 edited by Tom Goddard
(diff)
3:00 PM Ticket #20753 (The GPU device instance has been suspended) closed by Eric Pettersen
duplicate
2:57 PM Ticket #20752 (The GPU device instance has been suspended) closed by Eric Pettersen
duplicate
2:03 PM Ticket #20745 (Trac database down (was: Re: COD bond-perception bug)) closed by Eric Pettersen
fixed
1:05 PM Ticket #20755 (The GPU device instance has been suspended) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20754 (The GPU device instance has been suspended) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20753 (The GPU device instance has been suspended) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20752 (The GPU device instance has been suspended) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20751 (Failed to create D3D11 swapchain) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20750 (numpy bool no longer accepted by QCheckBox.setChecked()) created by Tristan Croll
[…]
1:05 PM Ticket #20749 (Save image/movie, no opengl context) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20748 (COD bond-perception bug) created by Tristan Croll
[…] [[Image(...)]]
1:05 PM Ticket #20747 (Movie: save duplicate images: No such file or directory) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #20746 (Corecif has metal coordination bonds only) created by Tristan Croll
[…] Description Picked up a new pathological case for corecif: …
12:09 PM Ticket #20745 (Trac database down (was: Re: COD bond-perception bug)) created by Greg Couch
[…]

Jul 11, 2026:

1:55 AM Ticket #20608 (ChatGPT use of ChimeraX: Python library missing) created by chimerax-bug-report@…
[…]

Jul 10, 2026:

6:50 PM Ticket #20607 (OpenFold prediction: "MMseqs2 API is giving errors", empty MSA gets ...) closed by Tom Goddard
fixed: Fixed. Tested the pinned requests 2.32.5 with ChimeraX openfold …
5:37 PM Ticket #20607 (OpenFold prediction: "MMseqs2 API is giving errors", empty MSA gets ...) created by goddard@…
[…]
4:33 PM Ticket #20572 (File Save dialog issues command without specifying "format" option) closed by Eric Pettersen
fixed: Fix: …
2:55 PM 2026-7-9 edited by Tom Goddard
(diff)
2:49 PM DeveloperMeetings edited by Tom Goddard
(diff)
2:07 PM Ticket #20551 (mmCIF handles non-orthogonal cells incorrectly) closed by Greg Couch
fixed: So Claude's bug was not a bug. So to_cartesian() has been reverted. …
1:57 PM Ticket #20604 (aniso_u6 not copied) closed by Eric Pettersen
fixed: Fixed in tomorrow's build. Fix: …
1:50 PM Ticket #20606 (Intersection operator (&) does not maintain atom ordering) created by mdmxd4@…
[…]
1:17 PM Ticket #20592 (Delay pyKVFinder install until absolutely necessary) closed by Eric Pettersen
fixed: Fixed in tomorrow's daily build. Fix: …
12:08 PM Ticket #20605 (glClear: invalid framebuffer operation drawing scene) created by pujanajmera1@…
[…]
11:50 AM Ticket #20538 (Problem restoring pseudo bonds in scenes) closed by Eric Pettersen
fixed: Fix: …
10:13 AM Ticket #20603 (Minimization failure: KeyError: 'N') closed by Eric Pettersen
can't reproduce: Works fine with the regular 6LUB entry, so would need file to reproduce.
10:07 AM Ticket #20602 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
9:40 AM Ticket #20604 (aniso_u6 not copied) created by Tristan Croll
[…]
12:34 AM Ticket #20603 (Minimization failure: KeyError: 'N') created by chimerax-bug-report@…
[…]

Jul 9, 2026:

9:03 PM Ticket #20602 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]
5:31 PM Ticket #20601 (Problem aligning structure and map) closed by Tom Goddard
not a bug: The x-ray map from the Electron Density Server (ChimeraX command "open …
1:43 PM Ticket #20595 (Session save: cannot import name 'get_session_info' from ...) closed by Eric Pettersen
duplicate: Hi Krish, This is the same problem you reported yesterday, and the …
11:08 AM Ticket #20601 (Problem aligning structure and map) created by openstomata@…
[…] PDB and eds.png​
10:45 AM Ticket #20600 (Minimization of RNA fails) created by bruno.haymele@…
Minimization of RNA fails, e.g. 9kgg and the file attached to this ticket.
5:24 AM Ticket #20599 (Problems installing ISOLDE) created by renato.weisse@…
[…]

Jul 8, 2026:

10:02 PM Ticket #20547 (Sequence viewer holding reference to deleted chain) closed by Eric Pettersen
fixed: Hi Mohammad, Thanks for reporting this problem. It is fixed in the …
5:24 PM Ticket #20598 (Make mutation score residue coloring use gray for unassociated residues) closed by Tom Goddard
fixed: Done.
5:20 PM Ticket #20598 (Make mutation score residue coloring use gray for unassociated residues) created by goddard@…
[…]
5:09 PM Ticket #20596 (Associating structure to mutation scores reports wrong alignment summary) closed by Tom Goddard
fixed: Fixed. It was reporting the number of associated residues with …
3:47 PM Ticket #20597 (Opening mutation score .csv file does not show the scores in the order ...) created by goddard@…
[…]
3:44 PM Ticket #20596 (Associating structure to mutation scores reports wrong alignment summary) created by goddard@…
[…]
12:06 PM Ticket #20593 (glClear: invalid framebuffer operation on statusbar expose) closed by Tom Goddard
duplicate: This ChimeraX error is fixed in the current ChimeraX 1.12 release. It …
11:58 AM Ticket #20595 (Session save: cannot import name 'get_session_info' from ...) created by rkrishnan@…
[…]
9:51 AM Ticket #20594 (Session save: cannot import name 'get_session_info' from ...) closed by Eric Pettersen
fixed: Hi Krish, Thanks for reporting this problem. It was fixed about a …
8:43 AM Ticket #20594 (Session save: cannot import name 'get_session_info' from ...) created by rkrishnan@…
[…]

Jul 7, 2026:

8:00 PM Ticket #20576 (Boltz requires older Python versions <= 3.12.) closed by Tom Goddard
fixed: Fixed. I made Boltz install use Astral Python 3.11 instead of the …
5:52 PM Ticket #20593 (glClear: invalid framebuffer operation on statusbar expose) created by iamkaant@…
[…]
2:08 PM 2026-7-9 created by Tom Goddard
2:07 PM DeveloperMeetings edited by Tom Goddard
(diff)
10:43 AM Ticket #20482 (Render by attribute configure: 'MarkedHistogram' object has no ...) closed by Eric Pettersen
fixed
9:46 AM Ticket #20592 (Delay pyKVFinder install until absolutely necessary) created by Tristan Croll
[…]
9:16 AM Ticket #20591 (Multiple consecutive Find Cavities: object of type ShortASLWidget has ...) closed by Eric Pettersen
can't reproduce
9:07 AM Ticket #20548 (Qt 6.11: saving image while floating windows break main window resize) closed by Zach Pearson
fixed: I rolled PyQt back to 6.10.2
9:06 AM Ticket #20590 (Main window resize broken with floating windows and PySide 6.11.1) closed by Zach Pearson
fixed
8:32 AM Ticket #20591 (Multiple consecutive Find Cavities: object of type ShortASLWidget has ...) created by chimerax-bug-report@…
[…]

Jul 6, 2026:

5:08 PM Ticket #20590 (Main window resize broken with floating windows and PySide 6.11.1) created by goddard@…
[…]
4:40 PM Ticket #16848 (Update from numpy 1 to numpy 2.) closed by Tom Goddard
fixed: Updated daily build to numpy 2.4.6. I tested most the major ChimeraX …
4:11 PM Dev2026-07-13 created by Tom Goddard
4:10 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:08 PM Dev2026-07-06 edited by Tom Goddard
(diff)
3:08 PM Ticket #20582 (Bug report - ChimeraX ("WARNING: GBM is not supported with the current ...) closed by Greg Couch
not a bug: This warning is an issue with the precompiled Qt UI toolkit that …
1:24 PM Ticket #4751 (Align trajectory frames) closed by Eric Pettersen
fixed: The …
12:42 PM Ticket #20589 (Crash in QPlatformIntegrationFactory::create) closed by Tom Goddard
can't reproduce: No idea what caused this crash at startup. The same ChimeraX started …
12:37 PM Ticket #20587 (glClear: invalid framebuffer operation on statusbar expose) closed by Tom Goddard
duplicate: This ChimeraX error was caused by a bug in the Qt window toolkit. The …
11:35 AM Ticket #20588 (ffmpeg: Permission denied) closed by Eric Pettersen
duplicate: Hi Jagriti, Thanks for reporting this problem. It has been fixed in …
11:12 AM Ticket #20586 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
11:11 AM Ticket #20585 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
11:11 AM Ticket #20584 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
11:10 AM Ticket #20583 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
11:07 AM Ticket #20579 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
11:03 AM Ticket #20577 (Proofpoint Essentials - Quarantine Digest) closed by Eric Pettersen
not a bug
5:06 AM Ticket #20589 (Crash in QPlatformIntegrationFactory::create) created by chimerax-bug-report@…
[…]

Jul 5, 2026:

10:29 AM Ticket #20588 (ffmpeg: Permission denied) created by jchander@…
[…]

Jul 4, 2026:

11:40 PM Ticket #20587 (glClear: invalid framebuffer operation on statusbar expose) created by pujanajmera1@…
[…]
1:03 AM Ticket #20586 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]

Jul 3, 2026:

5:02 PM Ticket #20585 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]
1:02 PM Ticket #20584 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]
9:02 AM Ticket #20583 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]
1:07 AM Ticket #20582 (Bug report - ChimeraX ("WARNING: GBM is not supported with the current ...) created by grimmerc@…
[…]

Jul 2, 2026:

7:38 PM Ticket #20573 (Boltz fails with numpy 2.4 due to numba requiring numpy version <= 2.1) closed by Tom Goddard
fixed: Fixed. Made Boltz prediction issue an error if the ChimeraX that …
6:22 PM Ticket #20581 (Interfaces toolbar icon error when atoms are selected) closed by Tom Goddard
fixed: Fixed. There is an "interfaces select" subcommand and that caused the …
5:43 PM Ticket #20581 (Interfaces toolbar icon error when atoms are selected) created by goddard@…
[…]
5:23 PM Ticket #20580 (Shader error raycasting with softlighting, volume, and molecule shown) created by goddard@…
[…]
5:02 PM Ticket #20579 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]
2:51 PM Ticket #20578 (isolde sim start: OpenMMException: Error compiling kernel) created by sahmed08@…
[…]
1:02 PM Ticket #20577 (Proofpoint Essentials - Quarantine Digest) created by do-not-reply@…
[…]
11:25 AM Ticket #20557 (Find Cavities crash in constitutional) closed by Eric Pettersen
fixed: The pyKVFinder authors have fixed this problem on their end, and I …
10:50 AM Ticket #20576 (Boltz requires older Python versions <= 3.12.) created by Tom Goddard
We plan to update ChimeraX to Python 3.14 after the update to numpy 2. …
4:12 AM Ticket #20575 (Unknown problem) created by disha-gajanan.hiregange@…
[…]

Jul 1, 2026:

10:13 PM Ticket #20574 (SEQCROW error reading NBO coefficients file: list index out of range) created by ud21003@…
[…]
3:48 PM Ticket #20573 (Boltz fails with numpy 2.4 due to numba requiring numpy version <= 2.1) created by goddard@…
[…]
12:52 PM Ticket #20564 (Several volume file readers use numpy fromstring() which does not work ...) closed by Tom Goddard
fixed: Fixed. I fixed numpy fromstring(), tostring(), int16 overflow, old …
12:50 PM Ticket #20572 (File Save dialog issues command without specifying "format" option) created by goddard@…
[…]
12:24 PM Ticket #20571 (Error reading Imaris .ims volume file with numpy 2) closed by Tom Goddard
fixed: Fixed. Replaced numpy tostring() with tobytes().
12:18 PM Ticket #20571 (Error reading Imaris .ims volume file with numpy 2) created by goddard@…
[…]
12:07 PM Ticket #20570 (Error reading netcdf with numpy2: AttributeError: 'MaskedArray' object ...) closed by Tom Goddard
fixed: Fixed. Replaced tostring() with tobytes().
11:58 AM Ticket #20566 (Netcdf file reading error with numpy 2: ValueError: numpy.dtype size ...) closed by Tom Goddard
fixed: Fixed. Updating netcdf4 PyPi package from version 1.6.5 to 1.7.4 …
11:56 AM Ticket #20570 (Error reading netcdf with numpy2: AttributeError: 'MaskedArray' object ...) created by goddard@…
[…]
11:51 AM Ticket #20568 (PyTables deprecation warning for dtype() align argument in numpy 2) closed by Tom Goddard
fixed: Fixed. Updated pytables from version 3.10.2 to 3.11.1 to fix numpy 2 …
11:43 AM Ticket #20565 (DCD file reader probably broken with numpy 2) closed by Tom Goddard
fixed
11:33 AM Ticket #20567 (Numeric overflow warning opening DSN6 .omap file with numpy 2) closed by Tom Goddard
fixed: Fixed. DSN6 uses int16 grid sizes and trying to compute the total …
11:19 AM Ticket #20569 (Trouble with ChimeraX 1.8) closed by Tom Goddard
can't reproduce: I suggest you try ChimeraX 1.12 available from SBGrid. It uses a …
6:57 AM Ticket #20569 (Trouble with ChimeraX 1.8) created by marjolaine.noirclerc@…
[…] [[Image(...)]]

Jun 30, 2026:

8:20 PM Ticket #20568 (PyTables deprecation warning for dtype() align argument in numpy 2) created by goddard@…
[…]
8:20 PM Ticket #20567 (Numeric overflow warning opening DSN6 .omap file with numpy 2) created by goddard@…
[…]
8:16 PM Ticket #20566 (Netcdf file reading error with numpy 2: ValueError: numpy.dtype size ...) created by goddard@…
[…]
7:47 PM Ticket #20565 (DCD file reader probably broken with numpy 2) created by Tom Goddard
The DCD file reader code md_crds/src/dcd/MDToolsMarch97/md_DCD.py …
7:43 PM Ticket #20564 (Several volume file readers use numpy fromstring() which does not work ...) created by goddard@…
[…]
7:42 PM Ticket #20562 (IMOD reader uses numpy array tostring() method removed in numpy 2) closed by Tom Goddard
fixed: Fixed. The numpy 1 tostring() method was a synonym for tobytes(). …
7:37 PM Ticket #20563 (IMOD file reader using numpy fromstring() where it needs frombuffer()) closed by Tom Goddard
fixed: Fixed. Use numpy frombuffer() instead of fromstring(), available in …
7:35 PM Ticket #20563 (IMOD file reader using numpy fromstring() where it needs frombuffer()) created by goddard@…
[…]
7:33 PM Ticket #20562 (IMOD reader uses numpy array tostring() method removed in numpy 2) created by goddard@…
[…]
7:29 PM Ticket #20561 (Error reading STL files with numpy 2) closed by Tom Goddard
fixed: Fixed. Use numpy frombuffer() instead of fromstring(), available in …
7:26 PM Ticket #20561 (Error reading STL files with numpy 2) created by goddard@…
[…]
7:22 PM Ticket #20560 (Opening gltf file with numpy 2 broken) closed by Tom Goddard
fixed: Fixed. Use numpy frombuffer() instead of fromstring(), available in …
7:14 PM Ticket #20560 (Opening gltf file with numpy 2 broken) created by goddard@…
[…]
6:25 PM Ticket #20559 (bool8 not in numpy2) closed by Tom Goddard
fixed
5:01 PM ChangeLog edited by Eric Pettersen
(diff)
4:56 PM Ticket #16310 (Port WriteDMS) closed by Eric Pettersen
fixed: Writing DMS files will be in tomorrow's daily build.
3:49 PM Ticket #20559 (bool8 not in numpy2) created by goddard@…
[…]
3:21 PM Ticket #16520 (Ribbon: Array argument has non-numeric values) closed by Tom Goddard
fixed: Finally got around to this change needed to support numpy 2. I made …
12:22 PM Ticket #20555 (Crash in QDockWidget::event() in ChimeraX 1.11.1) closed by Tom Goddard
duplicate: This is the usual Qt 6.9 ChimeraX 1.11.1 crash dragging a tool window. …
12:16 PM Dev2026-07-06 created by Tom Goddard
12:15 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:07 PM Ticket #20552 (MemoryError saving session with maps) closed by Tom Goddard
limitation: The ChimeraX session saving code currently copies the map data in …
11:59 AM Ticket #20558 (Avoid copying volumes to bytes when saving sessions) created by Tom Goddard
When ChimeraX includes volume data in a session file it first converts …
11:53 AM Ticket #20557 (Find Cavities crash in constitutional) created by charles.midgett@…
[…]
11:46 AM Ticket #20556 (SceneAnimation class goes into session files even when scenes and ...) created by goddard@…
[…]
9:42 AM Ticket #20553 (Session save: 'BlastProteinResults' object has no attribute 'table') closed by Eric Pettersen
duplicate: Hi Aleeza, Thanks for reporting this problem. It was fixed about 3 …
6:02 AM Ticket #20555 (Crash in QDockWidget::event() in ChimeraX 1.11.1) created by chimerax-bug-report@…
[…]
3:31 AM Ticket #20554 (Dead tool window still shown(?) [Qt 6.11?]) created by hamish.todd1@…
[…]

Jun 29, 2026:

6:10 PM Ticket #20553 (Session save: 'BlastProteinResults' object has no attribute 'table') created by aleeza.mughal@…
[…]
4:27 PM Dev2026-06-29 edited by Tom Goddard
(diff)
4:18 PM DeveloperMeetings edited by Tom Goddard
(diff)
3:36 PM Ticket #20552 (MemoryError saving session with maps) created by mahamaya@…
[…]
2:28 PM Ticket #20551 (mmCIF handles non-orthogonal cells incorrectly) created by Tristan Croll
[…] Description Little bug Claude came across while teaching …
2:25 PM Ticket #20546 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: The ChimeraX 1.9 crash you observed was caused by a bug in the Qt …